tbuckley/cabot-search huggingface dataset:
QOL-06. PREDICTING VENOUS THROMBOEMBOLISM IN PATIENTS WITH ADULT-TYPE DIFFUSE GLIOMAS
Authors: Kirsten B Burdett, Dusten Unruh, Michael Drumm, Jonathan Lamano, Margaret Schwartz, James Chandler, Rodrigo Javier, Alicia Steffens, Christina Amidei, Eric S Lipp, Katherine B Peters, Albert Lai, Blaine Eldred, Kathleen McCortney, Amy Heimberger, Denise Scholtens, Craig Horbinski
Journal: Neuro-Oncology (2022)

Abstract Venous thromboembolism (VTE) is a common paraneoplastic complication in patients with adult-type diffuse gliomas. VTE greatly diminishes quality-of-life, and can even be life-threatening. While effective VTE prediction models exist for other cancers, those models do not work for gliomas. Thus, there are no standard guidelines for thromboprophylaxis in glioma patients. To address this deficiency, arterial blood, tumor tissue, and comprehensive clinical-pathologic data (including next generation sequencing) were obtained from 258 newly diagnosed WHO grade 2-4 adult-type diffuse glioma patients at Northwestern Memorial Hospital. Forty-six out of 258 grade 2-4 glioma patients (17.8%) experienced a subsequent VTE. Intratumoral expression of two proteins that have been associated with VTE risk in other cancers, thromboplastin and podoplanin, was higher in IDH wild-type than IDH mutant gliomas. Tissue expression of both markers was associated with increased VTE risk, but in the circulation, only thromboplastin positively correlated with VTE. LASSO time-to-event analysis showed that older patient age, elevated body mass index, elevated WBC count, hypertension, a preoperative history of VTE, asthma, and higher WHO grade predicted increased postoperative VTE risk, whereas hypothyroidism, IDH mutation, and MGMT promoter methylation were negative risk factors. Together, these 10 variables generated a receiver operating characteristic curve for 3, 6, 9, and 12 months from original surgery resulting in estimated AUC value of 0.82 in the Northwestern discovery cohort, 0.72 in the UCLA validation cohort (N=68), and 0.68 in the Duke validation cohort (N=157). We created an online prediction tool based on this model, which estimates VTE risk up to 1 year from original surgery. To the best of our knowledge, this is the first externally validated VTE risk prediction tool designed specifically for adult-type diffuse glioma patients. This tool, based on readily obtainable information, provides treating physicians with more objective risk estimates on which to base thromboprophylaxis decision-making.
MODL-07. Sensitivity of Tumor Treating Fields (TTFields) treatment planning to tumor segmentation errors
Authors: Oshrit Ze’evi, Tal Marciano, Ariel Naveh
Journal: Neuro-Oncology (2022)

Abstract Tumor Treating Fields (TTFields) are electric fields that disrupt cellular processes critical for cancer cell viability and tumor progression. TTFields are administered through two pairs of capacitive arrays placed on the patient’s scalp. The effect of TTFields has been shown to be dose dependent. An in-silico study based on imaging and survival data from the phase 3 EF-14 study demonstrated a correlation between simulated field intensity and overall survival. Novocure is developing a simulation-based patient-specific treatment planning system aimed towards maximizing TTFields dose delivered to the patient’s tumor. Different options are presented to the treating physician that are ranked based on dose. To create patient-specific planning, physicians are required to segment the pathological tissues on a T1-weighted MRI. These tissues may include the enhancing tumors, resection cavity and necrotic core. Segmentation of medical images is an error-prone procedure. Such errors may influence the calculation of expected TTFields dose delivered to the tumors. In this work, we examined how different segmentations of the tumors affect the delivered dose, by placing mock tumors of different compositions within a simplified ellipsoidal model. Simulations were then used to assess field distributions in these tumors. Tumors of different enhanced volumes were then compared by LMiPD values. Our results show that 10% differences in the segmented enhancement result in less than 5% relative error in LMiPD. To enforce the validity of the simplified model, we performed the same analysis for two patient specific models. In both cases, the relative difference in segmentation was about 5%, and consequent errors in LMiPD was &amp;lt;5% as well. In conclusion, when using a simulation-based TTFields treatment planning system, small differences in the segmentation of the enhancing component of mock glioblastoma tumors in both simplified ellipsoid and patient specific models lead to small differences in LMiPD.
MODL-18. ORGANOTYPIC BRAIN SLICE CULTURES: A COMPREHENSIVE MODEL FOR PRIMARY CNS TUMOR STUDIES
Authors: Alexandra Reid
Journal: Neuro-Oncology (2022)

Abstract Inducing an immunosuppressive environment has been one of the most notable subversive tactics employed by aggressive primary brain tumors like Glioblastoma (GBM). It is vital that we garner a better understanding of the cell-cell interactions occurring within the tumor microenvironment (TME) in situ. Current in vitro and in vivo models sorely limit our ability to study the cell-cell interactions within the TME while accounting for its complexity and the spatial orientation of its components. Unfilled, this gap in physiologically relevant models greatly hinders the translation of impactful research findings to successful treatment options for patients diagnosed with GBM and other primary CNS tumors. We have devised a novel organotypic brain slice culture (BSC) model study using tumor-bearing C57BL/6J mice which brings the potential to not only determine the cell-cell interactions within the TME but also investigate the underlined mechanisms which govern them. Obtaining BSCs from tumor-bearing mice at various time points post-implantation also allows for analysis of the trafficking of various immune cells across the blood-brain barrier (BBB). We demonstrated outcomes similar to those seen in vivo following the introduction of parallel conditions, further supporting the physiological relevancy of this model. Thus, organotypic brain slice cultures from tumor-bearing mouse models may serve as a credible and incredibly versatile model for the study of primary CNS tumors which may bridge the gap between in vitro and in vivo studies.
CSIG-24. EPIGENETIC SUPPRESSION ALLOWS GBM TO MAINTAIN P53 WILD-TYPE STATUS
Authors: Jung Park, Michael Schulder, John Boockvar
Journal: Neuro-Oncology (2022)

Abstract Introduction Glioblastoma (GBM) is the most common primary brain malignancy in adults. The vast majority of GBM cases maintain wild-type status of p53, the protein considered to be the most critical tumor suppressor. How GBM displays such a malignant phenotype despite retaining normal p53 protein is unknown. We also aim to translate these molecular findings into therapeutics via a randomized clinical trial. METHODS A variety of molecular biological techniques were employed. These include CRISPR-CAS, next generation sequencing, stereotactic mouse brain injections, and histological analyses of human GBM tumors. Approval for a small, single site, blinded, randomized clinical trial for newly diagnosed GBM is underway. Overall survival, recurrence-free survival, immunohistochemical analyses will be assessed. RESULTS Human p53 wild-type GBM cell lines express Brd at higher levels compared to p53 mutant cell (~10 fold, p &amp;lt; 0.05). Cell viability assays show that deletion of Brd leads to a ~50% decrease (p &amp;lt; 0.05) in cell survival. Critically, this effect is abrogated upon deletion of p53 itself, showing that Brd functions through the inhibition of p53’s tumor suppressive effects. Furthermore, immunoprecipitation of Brd shows that it is a member of a complex of proteins that bind to p53 target genes. The importance of these findings are corroborated in vivo, as mice stereotactically injected with human GBM cells that lack Brd survive ~2-fold longer (p &amp;lt; 0.05) than mice that retain Brd. We have begun the process to start clinical trials with an already FDA-approved drug (currently used for the treatment of lymphoma and sarcoma) that blocks the Brd pathway. CONCLUSION Brd is the key suppressor of p53 target genes in GBM. Brd binds to a multimeric protein complex, which inhibits p53 target genes. Thus, the tumor suppressive effects of p53 are prevented in GBM. Inhibition of this pathway in GBM patients is underway.
PATH-15. THE PROGNOSTIC IMPLICATION OF MGMT PROMOTER METHYLATION IN IDH-MUTANT GLIOMAS
Authors: Gilbert Youssef, Elisa Aquilanti, Alona Muzikansky, Julie Miller, Jayne Vogelzang, Emily Lapinskas, Mary Jane Lim-Fat, Rifaquat Rahman, Rameen Beroukhim, Wenya Linda Bi, Ugonma Chukwueke, Luis Nicolas Gonzalez Castro, Eudocia Lee, J Ricardo McFaline-Figueroa, Lakshmi Nayak, David A Reardon, Keith Ligon, Patrick Y Wen
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND MGMT promoter methylation in IDH-mutant gliomas was associated with improved survival in a recent study (PMID 35386566) but did not account for the updated WHO classification of CNS tumors. We evaluated the prognostic value of MGMT methylation in IDH-mutant gliomas incorporating the 2021 WHO classification. METHODS We retrospectively identified 431 patients with IDH-mutant gliomas treated at a single institution from 2010-2020. Kaplan-Meier method was used to estimate OS and PFS rates. Log-Rank test was used to evaluate differences between groups. RESULTS Median age was 36.2 years. MGMT promoter was methylated in 49.6%, unmethylated in 17.2%, partially methylated in 6.7%, and untested in 26.5%. Histological diagnosis was consistent with astrocytoma in 45.7%, oligodendroglioma in 33.9%, glioblastoma in 16.4%, and oligoastrocytoma in 4%. After accounting for 1p/19q and CDKN2A statuses, 190 patients had an integrated diagnosis of astrocytoma, grade 2 or 3; 94 had astrocytoma, grade 4; and 147 had oligodendroglioma, grade 2 or 3. There were 101 death events. Median OS was 33.36 years and median PFS was 5.67 years in MGMT methylated gliomas, compared to median OS of 12.54 years (p=0.0064) and median PFS of 3.91 years (p=0.0034) in unmethylated tumors. Upon univariate subgroup analysis, MGMT methylation was associated with significantly longer OS in histological astrocytomas, grade 2 or 4. However, when stratifying patients according to 2021 WHO classification of CNS tumors, there was no significant difference in OS between MGMT methylated and unmethylated astrocytomas or oligodendrogliomas, irrespective of WHO grade. CONCLUSION MGMT promoter methylation was associated with prolonged OS in histological astrocytomas, IDH-mutant. However, MGMT status did not impact survival after incorporating 2021 WHO classification of CNS tumors, suggesting that 1p/19q co-deletion and CDKN2A homozygous deletion are stronger prognostic factors in our cohort. The number of survival events was limited; larger datasets are required for more definitive conclusions.
CTIM-16. PHASE 1 TRIAL OF RUXOLITINIB, TEMOZOLOMIDE, AND RADIATION IN HIGH-GRADE GLIOMAS
Authors: Manmeet Ahluwalia, Atulya Khosla, Yasmeen Rauf, Erin Murphy, Samuel Chao, John Suh, Glen Stevens, David Peereboom
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Ruxolitinib is a small molecule inhibitor of JAK1 (Janus kinase 1) and JAK2 and JAK3. Dysregulation of the JAK/STAT pathway is associated with increased proliferation and survival of malignant cells. Preclinical evidence supporting inhibition of the JAK-STAT pathway arrogated glioma growth led to the design of this trial. METHODS Newly diagnosed patients with unmethylated MGMT HGG (arm 1) received ruxolitinib and 60 Gy radiation for 6 weeks over 6 weeks (2Gy x 30). The dose of Ruxolitinib was administered given the 3 + 3 design. Level 1 was 10 mg twice daily, level 2 (15 mg twice daily), level 3 (20 mg twice daily), and level -1 was 5 mg twice daily. Patients with methylated MGMT HGG (arm 2) received ruxolitinib + radiation x 60 Gy + daily temozolomide at 75 mg/m2 for 6 weeks over 6 weeks. Overall survival (OS) and progression-free survival (PFS) were estimated by the Kaplan-Meier method and compared using the log-rank test. RESULTS 60 HGG were treated in the study and there was no dose-limiting toxicity. Survival data was calculated for 37 GBM patients. The OS for arm 1 was 18.17 months (10.15, NA) and was not reached for arm 2. The 1-year OS was 0.77 for all GBM patients, was 0.62 for arm 1 (unmethylated MGMT) and 0.93 for arm 2 (unmethylated MGMT). CONCLUSIONS A dose of 20 mg twice daily of ruxolitinib is safe with radiation and temozolomide. Preliminary survival data appears promising compared to the historical benchmarks for both the methylated MGMT and unmethylated MGMT groups. Genomic markers of response will be presented. A randomized phase 2 trial is planned.
PATH-36. GENOMIC MARKERS OF RECURRENCE RISK IN ATYPICAL MENINGIOMA FOLLOWING GROSS TOTAL RESECTION
Authors: Rachael Vaubel, Rahul Kumar, Taylor Weiskittel, Sarah Jenkins, Surendra Dasari, Joon Uhm, Daniel Honore Lachance, Paul Brown, Jamie Van Gompel, Benjamin Kipp, William Sukov, Caterina Giannini, Derek Johnson, Aditya Raghunathan
Journal: Neuro-Oncology (2022)

Abstract Atypical meningiomas (CNS WHO grade 2) show an intermediate risk of recurrence/progression, and molecular parameters informing management following gross total resection (GTR) remain to be established. We performed comprehensive genomic analysis in 63 patients who underwent GTR of an atypical meningioma. Median age was 59.8 years, 41 patients (65.1%) were female, and 8/62 patients (12.9%) underwent radiation therapy following resection. Follow-up was available for all patients (median 10 years), with recurrence/progression in 17 (5-year PFS: 84.2%; 10-year PFS: 71.0%). Tumors were evaluated by next generation sequencing (n=61), chromosomal microarray (n=63), DNA methylation profiling (n=62), and H3K27me3 immunohistochemistry (n=62). Next generation sequencing using a CLIA-certified 50-gene Neuro-Oncology specific panel identified pathogenic alterations in NF2 (n=31; 50.8%), SMARCB1 (n=5; 8.2%), AKT1 (n=2; 3.3%), TERT (n=1, 1.6%), SMO (n=1), SUFU (n=1), TP53 (n=1), and PTEN (n=1). There was trend toward decreased PFS in patients with NF2 alterations (p=0.078) which was not statistically significant. Copy number variants (CNVs) were identified using OncoScan (ThermoFisher). The most frequent CNVs were loss -22 (n=45; 71.4%), -1p (n=30, 47.6%), -14 (n=21, 33.3%), -6q (n=18, 28.6%), -10q (n=15, 23.8%), -X (n=13, 20.6%), and -18 (n=11, 17.4%). CNVs associated with decreased PFS included -1p (p=0.015), -7p (p=0.007), -10q (p=0.0007), and -18 (p=0.0376). DNA methylation profiling was performed using the Illumina MethylationEPIC array (n=62) and evaluated using the DKFZ classifier (v12.3). Based on the highest score, tumors matched to benign (n=32; 51.6%) or intermediate (n=29; 46.7%) meningioma subclasses or showed non-contributory profiles (n=1; 1.6%). Methylation class (benign vs. intermediate) showed no association with PFS (p=0.96). H3K27 trimethylation (H3K27me3) was unequivocally lost in 4 (6.5%) tumors, which was insufficient for PFS analysis. Overall, our study supports CNV profiling of atypical meningiomas following GTR, which can be implemented using existing, clinically validated technologies. Molecular predictors could guide use of radiotherapy in these patients.
MODL-16. SOMATICALLY ENGINEERED MOUSE MODELS RECAPITULATING CELLULAR AND MOLECULAR FEATURES OF HUMAN GBM
Authors: Joanna Pyczek, Bo Young Ahn, Heewon Seo, Samuel Lawn, Shannon Snelling, Katalin Osz, Robyn Flynn, Sorana Morrissy, Jennifer Chan
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Mouse models are instrumental in advancing our understanding of glioblastoma (GBM), however many commonly used models have features that limit their practicality or applicability. These limitations can include an incomplete immune context, a requirement for complex breeding strategies, high cost of specialized lines, and unpredictability in where tumors arise. We sought to develop and validate a mouse modeling system for some of the major human GBM subtypes that overcame these practical challenges. METHODS In vivo electroporation was used to introduce genetic alterations into periventricular cells of early postnatal C57Bl6/j mice. PiggyBac transposon/transposase and CRISPR-Cas9 systems were used to overexpress (OE) or knock out (KO) genes associated with mesenchymal (Nf1-KO/Pten-KO/p53-KO), classical (EGFRvIII-OE/Cdkn2a-KO/Pten-KO), and proneural (Pdgfra-OE/Cdk4-OE/p53-KO) IDH-WT GBM subtypes. KO or OE was confirmed by Indel Detection by Amplicon Analysis and immunofluorescent staining (IF). Tumours were analyzed for histologic, immunohistochemical, and transcriptional (RNAseq) features. RESULTS Tumors arose with near complete penetrance and median survivals of 36 to 116 days amongst models. All tumors were GFAP-expressing high-grade gliomas, with distinct phenotypes associated with different genetic combinations. Nf1-KO/Pten-KO/p53-KO tumors were composed of spindle cells. EGFRvIII-OE/Cdkn2a-KO/Pten-KO and Pdgfra-OE/Cdk4-OE/p53-KO tumors showed prevalence of small, round cells. Molecularly, Nf1-KO/Pten-KO/p53-KO tumors were enriched for human mesenchymal signature and displayed more differentiated phenotype. The Nf1-KO/Pten-KO/p53-KO model also showed increased stromal cells and macrophages. The other models had mixed proneural and classical profiles and were enriched for OPC- and NPC-like gene signatures found in human GBM. Once tumors formed, cells from each model were transplantable into C57Bl6/j mice to generate subsequent tumors. CONCLUSION We developed and validated a rapid, versatile, and reproducible system to model GBMs. These models allow for controlled study of GBM pathogenesis, progression, and treatment response, and allow for robust generation of syngeneic implantable mouse models that can serve as valuable tools for preclinical testing.
ANGI-08. EPIGENETIC REACTIVATION OF BAI1 SUPPRESSES TUMOR INVASION, RECURRENCE, AND SPINAL METASTASIS BY PREVENTING TGFΒ1-INDUCED MESENCHYMAL SWITCH IN GLIOBLASTOMA
Authors: Satoru Osuka, Liquan Yang, Hideharu Hashimoto, Dan Zhu, Zhaobin Zhang, Jeffrey Olson, Narra Devi, Erwin Van Meir
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is the most common and lethal type of malignant brain tumor in adults. GBM cells spread extensively in the brain and disseminate into the cerebrospinal fluid space, strongly restricting multimodal therapies. Acquiring a better knowledge of molecular defects underlying GBM invasion is essential for developing effective treatments.Brain-specific Angiogenesis Inhibitor 1 (BAI1/ADGRB1) is a transmembrane receptor of the adhesion GPCR family widely expressed in the normal brain, but its expression is lost in the majority of GBM through epigenetic silencing and restoration of its expression can inhibit glioma growth. However, whether BAI1 loss is important for tumor invasion and the mesenchymal phenotype in GBM has not been investigated.Microarray analysis of the GBM TCGA dataset (restricted to IDHwt GBM; WHO 2021) revealed that low BAI1 mRNA expression correlates with elevated expression of many mesenchymal genes. Restoration of BAI1 expression in human GBM cells suppresses mesenchymal gene expression in culture and dramatically decreases brain tumor invasion in mice xenografts. Mechanistically, we found that the N-terminal thrombospondin type 1 repeat (TSR#1) of BAI1 inhibits the maturation process of TGFβ1, a key growth factor involved in EMT. BAI1 is silenced epigenetically in GBM cells by methylated CpG-binding protein MBD2, and its expression can be reactivated by KCC-07, a blood-brain barrier permeable MBD2 inhibitor. We found that restoration of BAI1 expression by KCC-07 treatment dramatically suppresses cell invasion in the brain and reduces leptomeningeal dissemination of GBM cells to the spine in mouse xenografts.These experiments demonstrate that epigenetic silencing of BAI1 is important for activating the GBM invasive phenotype through TGFβ1 pathway activation. This new tumor-suppressive pathway can be epigenetically targeted to reactivate BAI1 expression in GBM patients.
TMIC-25. SPATIAL TRANSCRIPTOMIC LANDSCAPE OF DIFFUSE GLIOMA
Authors: Zhichao Wu, Karen Dazelle, Hye-Jung Chung, Kenneth Aldape
Journal: Neuro-Oncology (2022)

Abstract Single-cell studies have suggested heterogeneity of neoplastic cell states in diffuse gliomas. IDH-mutant astrocytoma and oligodendrogliomas (IDH-glioma) is described by cell states resembling including oligodendrocytes(OC), astrocytes (AC), and cycling neural progenitor cells (NPC); and IDH-wildtype glioblastoma (GBM-IDHwt) is marked by cell states resembling AC, NPC, oligodendrocyte progenitors (OPC) and mesenchymal (MES). Collective experience indicates that cell states are dynamic and can transition, at times recapturing brain development and inflammatory wound response. However, the spatial architecture of cell states, cell types and their interactions are yet to be investigated. We quantified the transcriptomics of 1,941 regions of interest (ROIs) from 19 IDH-glioma (non-1p/19q-codeleted n = 11, 1p/19q-codeleted n = 8) and 11 GBM-IDHwt tumors using the NanoString GeoMx Cancer Transcriptome Atlas (CTA, n = 1,811 genes) to study their spatial heterogeneity. Where appropriate, ROIs were selected to represent tumor core, infiltration edge, pseudopalisading necrosis, microvascular proliferation, and histological normal areas, if available. CTA profiling showed strong inter- and intra-tumor heterogeneity. Genes involved in oncogenesis and extra-cellular matrix such as VEGFA and VCAN, and macrophages (including CD74 and CCL3/1) showed the highest spatially variation. We identified substantial tumor immune environmental differences across ROIs including immune code, monocyte-like rich and lymphocyte-rich groups. The GBM-IDHwt cell states OPC and NPC were highly positively correlated (p-value = 5.65e-122) across ROIs suggesting spatial co-localization, but MES cell states were negatively correlated with the other three GBM cell states. M0 macrophage abundance was positively correlated with the MES state but negatively correlated with other cell states in GBM-IDHwt. The MES state was significantly lower in infiltrating edge of the tumor (p-value = 1.39e-34) but higher in the pseudopalisading necrosis region (p-value = 7.66e-30). Overall, this spatial transcriptomics dataset provides spatially informed relationships of neoplastic cell states and the immune microenvironment in diffuse glioma.